Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999912 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM144700)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:166892788C>TN/A show variant in all transcripts   IGV
HGNC symbol SCN1A
Ensembl transcript ID ENST00000375405
Genbank transcript ID NM_006920
UniProt peptide P35498
alteration type single base exchange
alteration region CDS
DNA changes c.3166G>A
cDNA.3184G>A
g.37362G>A
AA changes A1056T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1056
frameshift no
known variant Reference ID: rs2298771
databasehomozygous (T/T)heterozygousallele carriers
1000G15877752362
ExAC32206-31645561

known disease mutation at this position, please check HGMD for details (HGMD ID CM144700)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7210.012
-0.640
(flanking)-0.0970.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased37362wt: 0.56 / mu: 0.83wt: ATACAGCAGAAATTG
mu: ATACAACAGAAATTG		 ACAG|caga
Donor marginally increased37364wt: 0.7615 / mu: 0.7799 (marginal change - not scored)wt: ACAGCAGAAATTGGG
mu: ACAACAGAAATTGGG		 AGCA|gaaa
distance from splice site 231
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1056NKKDSCMSNHTAEIGKDLDYLKDV
mutated  not conserved    1056NKKDSCMSNHTTEIGKDLDYLKD
Ptroglodytes  not conserved  ENSPTRG00000012595  1067NKKDSCMSNHTTEIGKDLDYLKD
Mmulatta  not conserved  ENSMMUG00000008407  969DSCMSNHTTEIGKDLDYLKD
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000064329  1067NRKDNCISNHTTEIGKDLDCLKD
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000010095  1052NGKGNCISNHTSVEITKDPSG
Drerio  all identical  ENSDARG00000062744  1041SDGKENCLSNH-APVAVDLTKDYLKE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
10641064CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
10801080CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11461146CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11581161CONFLICTDIGA -> GHRR (in Ref. 2; AAK00217).might get lost (downstream of altered splice site)
12001514REPEATIII.might get lost (downstream of altered splice site)
12141237TRANSMEMHelical; Name=S1 of repeat III; (By similarity).might get lost (downstream of altered splice site)
12511276TRANSMEMHelical; Name=S2 of repeat III; (By similarity).might get lost (downstream of altered splice site)
12831304TRANSMEMHelical; Name=S3 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13091330TRANSMEMHelical; Voltage-sensor; Name=S4 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13501377TRANSMEMHelical; Name=S5 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13781378CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
13921392CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14031403CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14571483TRANSMEMHelical; Name=S6 of repeat III; (By similarity).might get lost (downstream of altered splice site)
15231821REPEATIV.might get lost (downstream of altered splice site)
15371537CONFLICTF -> L (in Ref. 7; CAA46439/M91803).might get lost (downstream of altered splice site)
15371560TRANSMEMHelical; Name=S1 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
15721595TRANSMEMHelical; Name=S2 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16021625TRANSMEMHelical; Name=S3 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16361657TRANSMEMHelical; Voltage-sensor; Name=S4 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16731695TRANSMEMHelical; Name=S5 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
17621786TRANSMEMHelical; Name=S6 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
17881788CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
19151944DOMAINIQ.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5997 / 5997
position (AA) of stopcodon in wt / mu AA sequence 1999 / 1999
position of stopcodon in wt / mu cDNA 6015 / 6015
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 19 / 19
chromosome 2
strand -1
last intron/exon boundary 4838
theoretical NMD boundary in CDS 4769
length of CDS 5997
coding sequence (CDS) position 3166
cDNA position
(for ins/del: last normal base / first normal base)		 3184
gDNA position
(for ins/del: last normal base / first normal base)		 37362
chromosomal position
(for ins/del: last normal base / first normal base)		 166892788
original gDNA sequence snippet GTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTT
altered gDNA sequence snippet GTTGTATGTCCAATCATACAACAGAAATTGGGAAAGATCTT
original cDNA sequence snippet GTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTT
altered cDNA sequence snippet GTTGTATGTCCAATCATACAACAGAAATTGGGAAAGATCTT
wildtype AA sequence MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN
LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI
AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL
EDFTFLRDPW NWLDFTVITF AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL
IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCIQW PPTNASLEEH SIEKNITVNY
NGTLINETVF EFDWKSYIQD SRYHYFLEGF LDALLCGNSS DAGQCPEGYM CVKAGRNPNY
GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM IFFVLVIFLG SFYLINLILA
VVAMAYEEQN QATLEEAEQK EAEFQQMIEQ LKKQQEAAQQ AATATASEHS REPSAAGRLS
DSSSEASKLS SKSAKERRNR RKKRKQKEQS GGEEKDEDEF QKSESEDSIR RKGFRFSIEG
NRLTYEKRYS SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAVFPANGK MHSTVDCNGV VSLVGGPSVP
TSPVGQLLPE GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR
QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP
MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN
VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL
FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV
FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY
EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS
VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS
SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC
FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW
VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE
GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN
NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP
KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM
KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT
ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS
PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN
FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS
VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV
WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF
TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL
KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK
PIVEKHEQEG KDEKAKGK*
mutated AA sequence MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN
LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI
AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL
EDFTFLRDPW NWLDFTVITF AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL
IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCIQW PPTNASLEEH SIEKNITVNY
NGTLINETVF EFDWKSYIQD SRYHYFLEGF LDALLCGNSS DAGQCPEGYM CVKAGRNPNY
GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM IFFVLVIFLG SFYLINLILA
VVAMAYEEQN QATLEEAEQK EAEFQQMIEQ LKKQQEAAQQ AATATASEHS REPSAAGRLS
DSSSEASKLS SKSAKERRNR RKKRKQKEQS GGEEKDEDEF QKSESEDSIR RKGFRFSIEG
NRLTYEKRYS SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAVFPANGK MHSTVDCNGV VSLVGGPSVP
TSPVGQLLPE GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR
QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP
MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN
VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL
FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV
FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY
EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTTEIGK DLDYLKDVNG TTSGIGTGSS
VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS
SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC
FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW
VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE
GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN
NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP
KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM
KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT
ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS
PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN
FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS
VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV
WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF
TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL
KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK
PIVEKHEQEG KDEKAKGK*
speed 0.88 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project